Improvement of physical, chemical, and biological properties of aridisol from Botswana by the incorporation of torrefied biomass

Bayesian network highlights the contributing factors for efficient arsenic phytoextraction by Pteris vittata in a contaminated field

Phytoextraction is a low-cost and eco-friendly method for removing pollutants, such as arsenic (As), from contaminated soil. One of the most studied As hyperaccumulators for soil remediation include Pteris vittata. Although phytoextraction using plant-assisted microbes has been considered a promising soil remediation method, microbial harnessing has not been achieved due to the complex and difficult to understand interactions between microbes and plants. This problem can possibly be addressed with a multi-omics approach using a Bayesian network. However, limited studies have used Bayesian networks to analyze plant-microbe interactions. Therefore, to understand this complex interaction and to facilitate efficient As phytoextraction using microbial inoculants, we conducted field cultivation experiments at two sites with different total As contents (62 and 8.9 mg/kg). Metabolome and microbiome data were obtained from rhizosphere soil samples using nuclear magnetic resonance and high-throughput sequencing, respectively, and a Bayesian network was applied to the obtained multi-omics data. In a highly As-contaminated site, inoculation with Pseudomonas sp. strain m307, which is an arsenite-oxidizing microbe having multiple copies of the arsenite oxidase gene, increased As concentration in the shoots of P. vittata to 157.5 mg/kg under this treatment; this was 1.5-fold higher than that of the other treatments. Bayesian network demonstrated that strain m307 contributed to As accumulation in P. vittata. Furthermore, the network showed that microbes belonging to the MND1 order positively contributed to As accumulation in P. vittata. Based on the ecological characteristics of MND1, it was suggested that the rhizosphere of P. vittata inoculated with strain m307 was under low-nitrogen conditions. Strain m307 may have induced low-nitrogen conditions via arsenite oxidation accompanied by nitrate reduction, potentially resulting in microbial iron reduction or the prevention of microbial iron oxidation. These conditions may have enhanced the bioavailability of arsenate, leading to increased As accumulation in P. vittata.

Improvement of rural soil properties and states by biomass carbon under the concept of sustainability: A research progress

Biomass carbon is a highly aromatic carbonaceous solid obtained by thermochemical reaction of biomass raw materials. It is frequently used in the research and application of soil properties and states improvement. Biomass carbon has abundant porous structure, high specific surface area and surface functional groups. After being applied to the soil, it has a significant impact on manipulating the physichemical properties of the soil, enhancing the microbial environment and remediating soil pollutants, which is conducive to the resource utilization of agricultural wastes and the long-term preservation of the environment. Based on 328 moderately to highly relevant literatures on biomass carbon and rural soil property improvement since 2010, this paper reviewed the contemporary research progress of biomass carbon application in soil property improvements utilizing the concept of sustainable development. In order to provide beneficial illumination for the complete implementation of biomass carbon in improving rural soil properties, this paper primarily evaluated the principle as well as mechanism of promoting sustainable soil properties. It tends to prospect the application and development aspirations of biomass carbon in soil ecological restoration, crop growth, development.

Sugarcane Metabolome Compositional Stability in Pretreatment Processes for NMR Measurements

Sugarcane is essential for global sugar production and its compressed juice is a key raw material for industrial products. Sugarcane juice includes various metabolites with abundances and compositional balances influencing product qualities and functionalities. Therefore, understanding the characteristic features of the sugarcane metabolome is important. However, sugarcane compositional variability and stability, even in pretreatment processes for nuclear magnetic resonance (NMR)-based metabolomic studies, remains elusive. The objective of this study is to evaluate sugarcane juice metabolomic variability affected by centrifugation, filtration, and thermal pretreatments, as well as the time-course changes for determining optimal conditions for NMR-based metabolomic approach. The pretreatment processes left the metabolomic compositions unchanged, indicating that these pretreatments are compatible with one another and the studied metabolomes are comparable. The thermal processing provided stability to the metabolome for more than 32 h at room temperature. Based on the determined analytical conditions, we conducted an NMR-based metabolomic study to discriminate the differences in the harvest period and allowed for successfully identifying the characteristic metabolome. Our findings denote that NMR-based sugarcane metabolomics enable us to provide an opportunity to collect a massive amount of data upon collaboration between multiple researchers, resulting in the rapid construction of useful databases for both research purposes and industrial use.

Chemometric Analysis of NMR Spectra and Machine Learning to Investigate Membrane Fouling

Efficient membrane filtration requires the understanding of the membrane foulants and the functional properties of different membrane types in water purification. In this study, dead-end filtration of aquaculture system effluents was performed and the membrane foulants were investigated via nuclear magnetic resonance (NMR) spectroscopy. Several machine learning models (Random Forest; RF, Extreme Gradient Boosting; XGBoost, Support Vector Machine; SVM, and Neural Network; NN) were constructed, one to predict the maximum transmembrane pressure, for revealing the chemical compounds causing fouling, and the other to classify the membrane materials based on chemometric analysis of NMR spectra, for determining their effect on the properties of the different membrane types tested. Especially, RF models exhibited high accuracy; the important chemical shifts observed in both the regression and classification models suggested that the proportional patterns of sugars and proteins are key factors in the fouling progress and the classification of membrane types. Therefore, the proposed strategy of chemometric analysis of NMR spectra is suitable for membrane research, which aims at investigating comprehensively the fouling phenomenon and how the foulants and environmental conditions vary according to the filtration systems.

Some Results of Poultry Litter Processing into a Fertilizer by the Wet Torrefaction Method in a Fluidized Bed

Poultry litter mass is formed in large quantities at poultry farms producing poultry meat (1–3 kg of litter mass per 1 kg of produced meat). These wastes represent a threat to the environment because of the presence of pathogenic microflora in them and the greenhouse gas emitted during the storage of these wastes. The procedure of poultry litter mass processing by wet torrefaction in a superheated water vapor environment at a temperature of 150–260 °C is studied. It is shown that after torrefaction at a temperature of 150 °C, the poultry litter mass retains high humidity, i.e., it represents an environment suitable for the re-development of pathogenic microflora. Only after wet torrefaction at a temperature of 260 °C does the humidity of the poultry litter mass decreases to 4%, and the risk of re-infection with pathogenic microflora decreases sharply. The absence of nitrates in the samples after torrefaction at a temperature of 260 °C indicates the termination of the activity of nitrifying bacteria. After torrefaction at a temperature of 260 °C, the poultry litter mass has a pH close to 7. This increases the mobility and availability of microelements for plants. Torrefaction at a temperature of 260 °C increases the content of ash, phosphorus and potassium by 30–40% and nitrogen by 15–20%, which makes the fertilizer more concentrated and optimizes the ratio of nitrogen, phosphorus and potassium. After wet torrefaction, due to the burning of the most easily degradable nitrogen-containing organic compounds and the destruction of some organophosphorus compounds, the mobility of nitrogen decreases, and the mobility of phosphorus increases. As a result of the research, it was found that the treatment of poultry manure by wet torrefaction in an environment of superheated water vapor at a temperature not lower than 260 °C makes it possible to obtain organic fertilizer with the most optimal nutrient content.

Agricultural Waste-Based Biochar for Agronomic Applications

Agricultural activities face several challenges due to the intensive increase in population growth and environmental issues. It has been established that biochar can be assigned a useful role in agriculture. Its agronomic application has therefore received increasing attention recently. The literature shows different applications, e.g., biochar serves as a soil ameliorant to optimize soil structure and composition, and it increases the availability of nutrients and the water retention capacity in the soil. If the biochar is buried in the soil, it decomposes very slowly and thus serves as a long-term store of carbon. Limiting the availability of pesticides and heavy metals increases soil health. Biochar addition also affects soil microbiology and enzyme activity and contributes to the improvement of plant growth and crop production. Biochar can be used as a compost additive and animal feed and simultaneously provides a contribution to minimizing greenhouse gas emissions. Several parameters, including biochar origin, pyrolysis temperature, soil type when biochar is used as soil amendment, and application rate, control biochar’s efficiency in different agricultural applications. Thus, special care should be given when using a specific biochar for a specific application to prevent any negative effects on the agricultural environment.

The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science

The environment, from microbial ecosystems to recycled resources, fluctuates dynamically due to many physical, chemical and biological factors, the profile of which reflects changes in overall state, such as environmental illness caused by a collapse of homeostasis. To evaluate and predict environmental health in terms of systemic homeostasis and resource balance, a comprehensive understanding of these factors requires an approach based on the "exposome paradigm", namely the totality of exposure to all substances. Furthermore, in considering sustainable development to meet global population growth, it is important to gain an understanding of both the circulation of biological resources and waste recycling in human society. From this perspective, natural environment, agriculture, aquaculture, wastewater treatment in industry, biomass degradation and biodegradable materials design are at the forefront of current research. In this respect, nuclear magnetic resonance (NMR) offers tremendous advantages in the analysis of samples of molecular complexity, such as crude bio-extracts, intact cells and tissues, fibres, foods, feeds, fertilizers and environmental samples. Here we outline examples to promote an understanding of recent applications of solution-state, solid-state, time-domain NMR and magnetic resonance imaging (MRI) to the complex evaluation of organisms, materials and the environment. We also describe useful databases and informatics tools, as well as machine learning techniques for NMR analysis, demonstrating that NMR data science can be used to evaluate the exposome in both the natural environment and human society towards a sustainable future.

Comparing straw, compost, and biochar regarding their suitability as agricultural soil amendments to affect soil structure, nutrient leaching, microbial communities, and the fate of pesticides

The emission of nutrients and pesticides from agricultural soils endangers natural habitats. Here, we review to which extent carbon-rich organic amendments help to retain nutrients and pesticides in agricultural soils and to reduce the contamination of surrounding areas and groundwater. We compare straw, compost, and biochar to see whether biochar outperforms the other two more traditional and cheaper materials. We present a list of criteria to evaluate the suitability of organic materials to be used as soil amendments and discuss differences in elemental compositions of straw, compost, and biochar to understand, how soil microorganisms utilize those materials. We review their effects on physical and chemical soil characteristics, soil microbial communities, as well as effects on the transformation and retention of nutrients and pesticides in detail. It becomes clear that for all three amendments their effects can vary greatly depending on numerous aspects, such as the type of soil, application rate, and production procedure of the organic material. Biochar is most effective in increasing the sorption capacity of soils but does not outperform straw and compost with regards to the other aspects investigated. Nevertheless, the possibility to design biochar properties makes it a very promising material. Finally, we provide critical comments about how to make studies about organic amendments more comparable (comprehensive provision of material properties), how to improve concepts of future work (meta-analysis, long-term field studies, use of deep-insight microbial DNA sequencing), and what needs to be further investigated (the link between structural and functional microbial parameters, the impact of biochar on pesticide efficiency).

Inoculation of Bacillus spp. Modulate the soil bacterial communities and available nutrients in the rhizosphere of vetiver plant irrigated with acid mine drainage

Acid mine drainage (AMD) is one of an important pollution sources associated with mining activities and often inhibits plant growth. Plant growth promoting bacteria has received extensive attention for enhancing adaptability of plants growing in AMD polluted soils. The present study investigated the effect of plant growth promoting Bacillus spp. (strains UM5, UM10, UM13, UM15 and UM20) to improve vetiver (Chrysopogon zizanioides L.) adaptability in a soil irrigated with 50% AMD. Bacillus spp. exhibited P-solubilization, IAA and siderophore production. The Bacillus spp. strains UM10 and UM13 significantly increased shoot (4.2-2.5%) and root (3.4-1.9%) biomass in normal and AMD-impacted soil, respectively. Bacillus sp. strain UM20 significantly increased soil AP (379.93 mg/kg) while strain UM13 increased TN (1501.69 mg/kg) and WEON (114.44 mg/kg) than control. Proteobacteria, Chloroflexi, Acidobacteria and Bacteroidetes are the dominant phyla, of which Acidobacteria (12%) and Bacteroidetes (8.5%) were dominated in soil inoculated with Bacillus sp. strain UM20 while Proteobacteria (70%) in AMD soil only. However, the Chao1 and evenness indices were significantly increased in soil inoculated with Bacillus sp. strain UM13. Soil pH, AP and N fractions were positively correlated with the inoculation of bacterial strains UM13 and UM20. Plant growth promoting Bacillus spp. strains UM13 and UM20 were the main contributors to the variations in the rhizosphere bacterial community structure, improving soil available P, TN, WEON, NO₃^--N thus could be a best option to promote C. zizanioides adaptability in AMD-impacted soils.

Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield

In 1840, Justus von Liebig proposed the theory of mineral plant nutrition, through the invention of the Haber–Bosch process, leading to the industrialization of chemical fertilizer (inorganic nitrogen) to feed the human population. Because the excessive use of chemical fertilizer has led to numerous environmental problems, understanding the agroecosystem that contains plants, microbes, and soils is necessary for sustainable agriculture. We revealed the network structure of an agroecosystem established with different management practices and identified that organic nitrogen is a key component contributing to crop yield under the condition of soil solarization, even in the presence of inorganic nitrogen. Our finding provides a potential solution to make crop production more sustainable by utilizing organic nitrogen induced by soil solarization.

Both inorganic fertilizer inputs and crop yields have increased globally, with the concurrent increase in the pollution of water bodies due to nitrogen leaching from soils. Designing agroecosystems that are environmentally friendly is urgently required. Since agroecosystems are highly complex and consist of entangled webs of interactions between plants, microbes, and soils, identifying critical components in crop production remain elusive. To understand the network structure in agroecosystems engineered by several farming methods, including environmentally friendly soil solarization, we utilized a multiomics approach on a field planted with Brassica rapa. We found that the soil solarization increased plant shoot biomass irrespective of the type of fertilizer applied. Our multiomics and integrated informatics revealed complex interactions in the agroecosystem showing multiple network modules represented by plant traits heterogeneously associated with soil metabolites, minerals, and microbes. Unexpectedly, we identified soil organic nitrogen induced by soil solarization as one of the key components to increase crop yield. A germ-free plant in vitro assay and a pot experiment using arable soils confirmed that specific organic nitrogen, namely alanine and choline, directly increased plant biomass by acting as a nitrogen source and a biologically active compound. Thus, our study provides evidence at the agroecosystem level that organic nitrogen plays a key role in plant growth.

Biomass torrefaction: An overview on process parameters, economic and environmental aspects and recent advancements

Torrefaction is one of the pretreatment processes used to overcome the disadvantages of using biomass as a fuel such as low energy density, high moisture, and oxygen contents. The torrefaction increases energy density, hydrophobicity, and reduces grinding energy requirement of biomass. This paper provides a review of the recent advancements in the torrefaction process. The discussion will cover the environmental and economic aspects of the torrefaction process and torrefied pellets, and various applications of torrefaction products. The cost competitiveness of torrefied pellets is one of the major concern of the torrefaction process. Integrating the torrefaction with other processes makes it economically more viable than as a standalone process.

Use of Carbonized Fallen Leaves of Jatropha Curcas L. as a Soil Conditioner for Acidic and Undernourished Soil

Jatropha (Jatropha curcas L.) represents a renewable bioenergy source in arid regions, where it is used to produce not only biodiesel from the seed oil, but also various non-oil biomass products, such as fertilizer, from the seed cake following oil extraction from the seeds. Jatropha plants also generate large amounts of fallen leaves during the cold or drought season, but few studies have examined the utilization of this litter biomass. Therefore, in this study, we produced biochar from the fallen leaves of jatropha using a simple and economical carbonizer that was constructed from a standard 200 L oil drum, which would be suitable for use in rural communities, and evaluated the use of the generated biochar as a soil conditioner for the cultivation of Swiss chard (Beta vulgaris subsp. cicla “Fordhook Giant”) as a model vegetable in an acidic and undernourished soil in Botswana. Biochar application improved several growth parameters of Swiss chard, such as the total leaf area. In addition, the dry weights of the harvested shoots were 1.57, 1.88, and 2.32 fold higher in plants grown in soils containing 3%, 5%, and 10% biochar, respectively, compared with non-applied soil, suggesting that the amount of biochar applied to the soil was positively correlated with yield. Together, these observations suggest that jatropha fallen leaf biochar could function as a soil conditioner to enhance crop productivity.

InterSpin: Integrated Supportive Webtools for Low- and High-Field NMR Analyses Toward Molecular Complexity

InterSpin (http://dmar.riken.jp/interspin/) comprises integrated, supportive, and freely accessible preprocessing webtools and a database to advance signal assignment in low- and high-field NMR analyses of molecular complexities ranging from small molecules to macromolecules for food, material, and environmental applications. To support handling of the broad spectra obtained from solid-state NMR or low-field benchtop NMR, we have developed and evaluated two preprocessing tools: sensitivity improvement with spectral integration, which enhances the signal-to-noise ratio by spectral integration, and peaks separation, which separates overlapping peaks by several algorithms, such as non-negative sparse coding. In addition, the InterSpin Laboratory Information Management System (SpinLIMS) database stores numerous standard spectra ranging from small molecules to macromolecules in solid and solution states (dissolved in polar/nonpolar solvents), and can be searched under various conditions using the following molecular assignment tools. SpinMacro supports easy assignment of macromolecules in natural mixtures via solid-state ¹³C peaks and dimethyl sulfoxide-dissolved ¹H-¹³C correlation peaks. InterAnalysis improves the accuracy of molecular assignment by integrated analysis of ¹H-¹³C correlation peaks and ¹H-J correlation peaks of small molecules dissolved in D₂O or deuterated methanol, which supports easy narrowing down of metabolite candidates. Finally, by enabling database interoperability, SpinLIMS's client software will ultimately support scientific discovery by facilitating sharing and reusing of NMR data.

Getting to the root of the matter: Water-soluble and volatile components in thermally-treated biosolids and biochar differentially regulate maize (Zea mays) seedling growth

The use of thermally treated biomass, including biochar, as soil amendments can improve soil fertility by providing nutrients, stable C and improving soil water-holding capacity. However, if the degree of carbonization is low, these soil amendments can lower crop productivity as a result of high salinity or organic compounds. The overall effect of these soil amendments is mediated by complex relationships between production conditions, soil properties and environmental conditions. This study aimed to 1) characterize the physiochemical properties and organic compounds released by three soil amendments (softwood biochar or pyrogenic carbonaceous biosolids), 2) determine the effects of these amendments on maize (Zea mays) seedling productivity, and 3) relate properties of these amendments to effects on maize seedling productivity under controlled environment conditions. Physicochemical properties and mobile organic compounds (water-soluble and volatile organic compounds were determined. The amendments were tested in maize germination and greenhouse experiments. Chemical fingerprinting of volatile and water-soluble compounds revealed over 100 mobile organic species. Increasing treatment temperature from 270 to 320°C reduces phytotoxicity of pyrogenic carbonaceous biosolids soil amendments. Water-soluble components of pyrogenic carbonaceous biosolids produced at 270°C (inorganic N, Na and/or organic compounds) were associated with reduced maize seedling productivity. Volatile components of pyrogenic carbonaceous biosolids produced at 320°C were associated with improved maize seedling productivity; nitrogen uptake was increased in spite of smaller root systems as a result of increased mineralization of soil or amendment N and/or uptake of organic N compounds. These results suggest that pyrogenic carbonaceous biosolids have potential benefits to provide plant nutrients when the amount of organic and inorganic species are limited during early growth stages, under greenhouse conditions. Future studies should examine these effects under field conditions to confirm whether controlled environment results translate into effects on yield.

Environmental metabolomics with data science for investigating ecosystem homeostasis

A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.

Potential of miscanthus biochar to improve sandy soil health, in situ nickel immobilization in soil and nutritional quality of spinach

The complex interaction of biochar (BC) with soil health reflecting properties, the feedstock used to prepare BC and application rate of BC in sandy soil is still a question for the researchers. An incubation study was conducted where nine different sorts of BC, each prepared from the different feedstock, were applied at 2% rate to evaluate their relative suitability to improve sandy soil health. Results revealed that BC prepared from miscanthus (MIB) significantly increased soil medium and fine pores, available water content (AWC), electrical conductivity (EC), and cation exchange capacity (CEC) while decreased soil wide pores, pH, bulk density (BD) and particle density (PD) compared to the rest sorts of BC. Later, spinach was grown in pots containing same soil but spiked with 50 ppm nickel (Ni) and amended with 1, 2, 3, 4 and 5% rates of MIB. The results showed a significant increment in spinach biomass, reduction in the concentrations of Ni in spinach tissues and DTPA-extractable Ni with the increasing rate of MIB till 3% and later, no significant changes with 4 and 5% rates thereafter. However, significant improvement in the activities of antioxidant enzymes, chemical and biochemical attributes of spinach were observed at 5% MIB when compared to lower rates. Similarly, post-harvest soil physicochemical and enzymatic parameters were also significantly (P < 0.05) improved with increasing rates of MIB. This study implies that application of MIB at 5% rate can improve the nutritional quality of spinach, sandy soil health and can reduce Ni concentrations in spinach tissues.